DNA-dependent DNA polymerases containing proof-reading activity have to coordinate two catalytic activities: the DNA polymerase activity and the exonuclease activity. For polymerase I type DNA polymerases (E. coli Pol I) as well as for B-type DNA polymerases, these catalytic activities are located on structurally distinct protein domains (Truniger, V., Lázaro, J., Salas, M. and Blanco, L. (1996) EMBO J., 15(13), 3430-3441; Pisani, F. M., De Felice, M. and Rossi, M. (1998) Biochemistry, 37(42), 15005-15012). In B-type (eukaryotic-type) DNA polymerases, the coordination of the two catalytic activities was proposed to take place intramolecularly in the conserved motif Y-GG/A located between the N-terminal 3′-5′ exonuclease and the C-terminal polymerization domain (Truniger, V., Lázaro, J., Salas, M. and Blanco, L. (1996) EMBO J., 15(13), 3430-3441; Pisani, F. M., De Felice, M. and Rossi, M. (1998) Biochemistry, 37(42), 15005-15012). For the Klenow fragment of E. coli DNA polymerase it was described, that the editing can be an intermolecular or intramolecular process involving dissociation and reassociation of the DNA depending on the local context (Joyce, C. M. (1989) JBC, 264(18), 10858-10866). Truniger et al. (Truniger, V., Lázaro, J., Salas, M. and Blanco, L. (1996) EMBO J., 15(13), 3430-3441) demonstrated for the mesophile replicative DNA polymerase of bacteriophage φ29 that mutations in the Y-GG/A motif can lead to phenotypes favoring either polymerisation or exonucleolysis compared to the wild type enzyme. They could show that this effect is related to altered (ss)DNA binding parameters and that the motif is important for the communication between the polymerase and exonuclease active site in a combination of structural and functional roles.
For the DNA polymerase of the thermophilic crenarchaeon Sulfolobus solfataricus (Sso) a region of 70 amino acids (region 1) involved in enzyme-DNA interaction was determined (Pisani, F. M., Manco, G., Carratore, V. and Rossi, M. (1996) Biochemistry, 35, 9158-9166). It is located in the connecting part between the exonuclease domain and the polymerase domain and contains the Y-GG/A motif. By mutational analysis of the amino acids in the Y-GG/A motif, it could be shown that the amino acids in this part of the enzyme determine the processivity of the proofreading function (Pisani, F. M., De Felice, M. and Rossi, M. (1998) Biochemistry, 37(42), 15005-15012). Based on the crystal structure of bacteriophage RB69 DNA polymerase, Truniger et al. proposed a direct interaction of the tyrosine with the phosphodiester bond between the two nucleotides preceding the one acting as template (Truniger, V., Blanco, L. and Salas, M. (1999) J. Mol. Biol., 286, 57-69).